STATE OF HAWAII SARS-COV-2 SEQUENCING AND VARIANT REPORT - HAWAII DEPARTMENT OF HEALTH 2022-01-28
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State of Hawaii SARS-CoV-2 Sequencing and Variant Report
Hawaii Department of Health
2022-01-28
1Contents
Introduction 3
Acknowledgements 4
County distribution of genomes sequenced by State Laboratories Division since Jan 1st,
2021 4
Summary and key notes 5
Significance of variants of concern and variants being monitored 6
Variants of concern (VOC) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Delta variant (B.1.617.2 and AY.* sub-lineages) . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Omicron variant (B.1.1.529 and BA.* sub-lineages) . . . . . . . . . . . . . . . . . . . . . . . . 6
Variants being monitored (VBM) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Alpha variant (B.1.1.7 and Q.* sub-lineages) . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Gamma variant (P.1 and P.1.* sub-lineages) . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Beta variant (B.1.351 and B.1.351.* sub-lineages) . . . . . . . . . . . . . . . . . . . . . . . . . 7
Mu variant (B.1.621 and B.1.621.1) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Iota variant (B.1.526) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Epsilon variant (B.1.429 and B.1.427) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
State of Hawaii 8
Total variants identified . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Estimate of proportion of variants circulating in the State of Hawaii . . . . . . . . . . . . . . . . . 9
Variants of concern in the State of Hawaii . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Variants being monitored in the State of Hawaii . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Honolulu County 12
Total variants identified in Honolulu County . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Estimate of proportion of variants circulating in Honolulu County . . . . . . . . . . . . . . . . . . 13
Variants of concern in Honolulu County . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
Variants being monitored in Honolulu County . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Maui County 16
Total variants identified in Maui County . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Estimate of proportion of variants circulating in Maui County . . . . . . . . . . . . . . . . . . . . . 17
Variants of concern in Maui County . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Variants being monitored in Maui County . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Hawaii County 20
Total variants identified in Hawaii County . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Estimate of proportion of variants circulating in Hawaii County . . . . . . . . . . . . . . . . . . . . 21
Variants of concern in Hawaii County . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Variants being monitored in Hawaii County . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Kauai County 24
Total variants identified in Kauai County . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Estimate of proportion of variants circulating in Kauai County . . . . . . . . . . . . . . . . . . . . 25
Variants of concern in Kauai County . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Variants being monitored in Kauai County . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
2Introduction
Whole genome sequencing (WGS) involves a set of laboratory methods used to determine the full genome
sequence of an organism or virus, which in the case of Severe Acute Respiratory Syndrome Coronavirus 2
(SARS-CoV-2), the virus that causes Coronavirus Disease 2019 (COVID-19), is approximately 30,000 letters,
each letter being one of A, C, G, or T.
The genome sequence of a virus can reveal mutations that make it unique. Mutations are changes in a genome
sequence (usually one-letter changes) and occur naturally over time.
Collecting the genome sequences of virus specimens can reveal information about the relatedness of viruses
and the similarities shared among groups of viruses. Groups of same-species viruses that share a set of
genome mutations are referred to as a lineage.
Scientists compare viral genomes to better understand virus transmission, how viruses can spread from
person to person. Sequencing also allows Public Health Officials to monitor viruses involved in outbreaks,
characterize outbreaks, detect clusters of cases, and monitor new lineages. Novel mutations can emerge with
new lineages and scientists refer to these new lineages as emerging variants.
Some of these variants are classified by the Centers for Disease Control and Prevention (CDC) as variants
of concern and others as variants being monitored, because of their attributes, which, for example, can
be increased transmissibility, decreased neutralization by antibodies generated during previous infection or
vaccination, or increased severity of disease. The CDC has extensive information about SARS-CoV-2 variant
classification (https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/variant-surveillance/variant-in
fo.html), which is updated as new evidence becomes available.
Sequencing can only be performed on samples that contain SARS-CoV-2 RNA, which means only samples
used for molecular tests (such as PCR) can be included. Therefore, this report is limited to confirmed
PCR-positives only. The genomes that are sequenced and compared are those of the virus, not humans.
Sequencing can be performed on stored specimens at any time. Therefore, the dataset used for this report is
dynamic and batches of stored specimens that are newly sequenced will be added to the dataset as sequencing
occurs. Because of this, trends based on historical data can change over time.
The State of Hawaii has conducted sequencing on approximately 5% of positive specimens since testing began,
according to the CDC (https://covid.cdc.gov/covid-data-tracker/#published-sars-cov-2-sequences).
In February 2021, State Laboratories Division, Hawaii Department of Health increased sequencing efforts
done on positive samples to improve the State’s ability to detect new variants of concern and variants being
monitored.
3Acknowledgements
This report integrates genomes sequenced since Jan 1, 2021 by:
Institution Program/partner Count Percent
Laboratory Preparedness and Response 6453 79.304%
Branch, State Laboratories Division
Centers for Disease Control and Prevention National SARS-CoV-2 Strain 278 3.416%
Surveillance (NS3)
Quest Diagnostics 433 5.321%
Incorporated
Laboratory Corporation of 352 4.326%
America
Aegis Sciences Corporation 215 2.642%
Helix/Illumina 68 0.836%
Infinity Biologix 15 0.184%
Mako Medical 9 0.111%
Fulgent Genetics 6 0.074%
Tripler Army Medical Center 308 3.785%
Total 8137 100.000%
Table Notes:
• The samples sequenced by the CDC for the National SARS-CoV-2 Strain Surveillance (NS3) program
are collected, quality controlled, and shipped to the CDC by the Laboratory Preparedness and Response
Branch (LPRB), State Laboratories Division, Hawaii Department of Health.
County distribution of genomes sequenced by State Laboratories
Division since Jan 1st, 2021
Honolulu County Maui County Hawaii County Kauai County unknown Total
3906 867 1048 322 310 6453
Table Notes:
• County information is unavailable or “unknown” for a number of samples sequenced by State Laboratories
Division. Furthermore, county information is not provided for samples sequenced by the CDC and its
commercial partners, and by Tripler Army Medical Center (TAMC).
4Summary and key notes
• State Laboratories Division has reported an additional 344 sequenced SARS-CoV-2 genomes since the
previous variant report was generated (1/14/2022).
• The CDC and its commercial partners have reported an additional 139 sequenced SARS-CoV-2 genomes
from the State of Hawaii since the previous variant report was generated (1/14/2022).
• TAMC has reported 1 additional sequenced SARS-CoV-2 genome from the State of Hawaii since the
previous variant report was generated (1/14/2022).
• SARS-CoV-2 variant nomenclature is defined by a World Health Organization (WHO) label (letters of
the Greek Alphabet, i.e., Alpha, Beta, Gamma, Delta, etc.), Pango lineage (alphabetical prefix and a
numerical suffix), and/or Nextstrain clade (year of emergence followed by a letter ordered alphabetically
by emergence, i.e., 20A, 20B, etc.). In this report, variant counts are reported using the WHO label
and Pango lineage (or “Lineage”) nomenclatures only.
• Classifications of Delta lineages are in flux. Since the previous report, a significant proportion of Delta
genomes previously classified as parent lineage B.1.617.2 have been reclassified as an AY.* sub-lineage.
Furthermore, for simplicity, not all AY.* sub-lineages identified in the State of Hawaii or its counties are
outlined in the Tables on the following pages, and instead are included as “Other AY.*” under Lineage.
• Classifications of Omicron lineages are in flux. Since the previous report, a significant proportion of
Omicron genomes previously classified as sub-lineage BA.1 have been reclassified as sub-lineage BA.1.1.
With this reclassification, BA.1.1 has been more prevalent than BA.1 in the State of Hawaii since the
Omicron wave began; however, the comparative proportions of BA.1 and BA.1.1 among total Omicron
detected in the State have remained steady since Omicron became the dominant variant.
• The Omicron sub-lineage BA.2, which was first detected in South Africa in late November 2021 and
subsequently classified in early December 2021, has recently been detected in the State of Hawaii. BA.2
has reportedly outpaced BA.1 and BA.1.1 to become the dominant Omicron variant in some countries,
and thus is suspected of being more infectious than BA.1 and BA.1.1. However, there are no scientific
data published to date to indicate whether transmissibility differs between Omicron lineages.
5Significance of variants of concern and variants being monitored
It is important to note that evidence to date shows that vaccination leads to milder cases, not requiring
hospitalization, for all variants of concern and variants being monitored that are described here, even if the
efficacy of antibodies is diminished against some of these variants compared to the original version of the
virus.
Also, none of these variants are classified as a “variant of high consequence”, according to CDC variant
categories (https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-info.html#Consequence), which is
a category that would imply a variant has the ability to evade diagnosis, significantly reduce the vaccines
effectiveness and protection against severe disease, significantly reduce susceptibility to treatments, or lead to
more severe disease and increased hospitalizations.
Variants of concern (VOC)
Delta variant (B.1.617.2 and AY.* sub-lineages)
B.1.617.2 was first identified in India and the WHO labeled it “Delta” on May 31, 2021. This variant contains
the L452R mutation in the spike protein, which has been shown to escape neutralization by monoclonal
antibodies and some convalescent sera, as well as a few additional spike mutations predicted to have functional
consequences (e.g. T478K). The Delta variant is highly contagious, more than 2x as contagious as previous
variants. The Delta variant is also known as Nextstrain clade 21A, 21I, and 21J. For more information about
Delta, go to (https://www.cdc.gov/coronavirus/2019-ncov/variants/delta-variant.html).
Omicron variant (B.1.1.529 and BA.* sub-lineages)
B.1.1.529 was reported to the WHO on November 24, 2021 and first detected in specimens collected on
November 11, 2021 in Botswana and on November 14, 2021 in South Africa. The WHO named the B.1.1.529
“Omicron” and classified it as a VOC on November 26, 2021. The United States designated Omicron
as a VOC on November 30, 2021 and reported its first case on December 1, 2021. Omicron contains
more changes in the spike protein than have been observed in other variants, including at least 30 amino
acid substitutions (15 of these are in the receptor binding domain), three small deletions, and one small
insertion. Several of these mutations, including S477N, N501Y, and E484K, have been associated with
increased infectivity and decreased neutralizing activity of monoclonal antibodies and convalescent sera.
Evidence suggests that Omicron is more transmissible and more immune evasive than previous variants,
and that immunity conferred by prior infection or vaccination may be reduced compared to Delta; however,
the clinical severity of Omicron infection compared to previous variants remains unclear. The Omicron
variant is also known as Nextstrain clade 21M, 21K, and 21L. For more information about Omicron, go to
(https://www.cdc.gov/coronavirus/2019-ncov/variants/omicron-variant.html; https://www.cdc.gov/coronavi
rus/2019-ncov/science/forecasting/mathematical-modeling-outbreak.html).
Variants being monitored (VBM)
Alpha variant (B.1.1.7 and Q.* sub-lineages)
B.1.1.7 was first identified in the United Kingdom and the WHO labeled it “Alpha” on May 31, 2021. This
variant contains the N501Y mutation and a short deletion in the spike protein. This variant is concerning
because it has been shown to be significantly more transmissible (~50%) than the original SARS-CoV-2 lineages
and reports from the United Kingdom suggest that B.1.1.7 cases are more likely to require hospitalization.
B.1.1.7 does not appear to evade vaccine-induced neutralizing antibody responses. The Alpha variant is also
known as Nextstrain clade 20I.
6Gamma variant (P.1 and P.1.* sub-lineages)
P.1 was first identified in Brazil and the WHO labeled it “Gamma” on May 31, 2021. This variant also
contains the N501Y mutation, like B.1.1.7, but not the deletion in the spike protein. Preliminary studies
suggest that antibodies from previous infection or from vaccination may be less effective at preventing
infection against this variant. The Gamma variant is also known as Nextstrain clade 20J.
Beta variant (B.1.351 and B.1.351.* sub-lineages)
B.1.351 was first identified in South Africa and the WHO labeled it “Beta” on May 31, 2021. This variant is
highly infectious and can quickly spread from person to person. Preliminary studies suggest that antibodies
from previous infection or from vaccination may be less effective at preventing infection against this variant
due to presence of the E484K mutation in the spike protein. The Beta variant is also known as Nextstrain
clade 20H.
Mu variant (B.1.621 and B.1.621.1)
Lineage B.1.621 was first identified in Columbia in January 2021 and it has a couple of mutations in common
with the Beta (B.1.351) and Gamma (P.1) variants, which have been associated with high transmissibility
(N501Y) and a level of decreased vaccine efficiency (E484K). The MU variant is also known as Nextstrain
clade 21H.
Iota variant (B.1.526)
B.1.526 was first identified in New York and is classified by CDC as a VBM because of indications that it has
increased transmissibility. The WHO labeled it “Iota” on May 31, 2021. Some of the samples (but not all) of
this variant contain the E484K mutation. The Iota variant is also known as Nextstrain clade 21F.
Epsilon variant (B.1.429 and B.1.427)
The closely related lineages, B.1.429 and B.1.427, were first identified in California and designated initially as
CA VUI1. The WHO labeled them “Epsilon” on May 31, 2021. They can quickly spread from person-to-
person, with an estimated ~20% higher efficiency than the original virus. The CDC has deescalated Epsilon
from a VOC to VBM on June 29, 2021, due to the significant decrease in the proportion of B.1.429/B.1.427
lineage viruses circulating nationally, as well as the available data indicating that vaccines and treatments are
effective against this variant. CDC removed B.1.429 and B.1.427 from the VBM list in July 2021 due to
declining prevalence. The Epsilon variant is also known as Nextstrain clade 21C.
7State of Hawaii
Total variants identified
27%
26%
22%
% of PCR−positive cases sequenced
21% 21%
20
Lineage
10 10% B AY.5.3 AY.42 AY.114
9.2%
B.1.1 AY.9.2 AY.43 AY.116.1
B.1.637 AY.13 AY.44 AY.117
5.9% 5.8% B.1.1.529 AY.14 AY.46.4 AY.118
4.8%
BA.1 AY.20 AY.47 AY.119
2% BA.1.1 AY.23 AY.48 AY.119.2
0.59% BA.2 AY.25 AY.54 AY.120
0
B.1.1.7 AY.25.1 AY.64 AY.120.1
600 Q.3 AY.26 AY.74 AY.121
B.1.617.2 AY.29 AY.75 AY.122
AY.2 AY.34.1 AY.77 AY.125
AY.3 AY.34.2 AY.81 AY.126
AY.3.1 AY.35 AY.100 AY.127
AY.4 AY.36 AY.103 B.1.351
400
AY.4.5 AY.37 AY.105 B.1.621
Viruses sequenced
AY.4.10 AY.39 AY.110 B.1.621.1
AY.5 AY.39.1 AY.113
200
0
4 28 11 25 09 23 06 20 04 18 01 15
−1 8− 9− 9− 0− 0− 1− 1− 2− 2− 1− 1−
08 −0 −0 −0 −1 −1 −1 −1 −1 −1 −0 −0
2 1− 21 21 21 21 21 21 21 21 21 22 22
20 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0 2 0
2−week period ending on date
Figure Notes:
• The graph shows the total number of variants by lineage detected in the State of Hawaii in each 2-week
interval ending on the date shown (date represents when the specimen was collected from a patient).
• Variants of concern shown are Delta (lineages B.1.617.2 + AY.*) and Omicron (lineages B.1.1.529 +
BA.*).
• Variants being monitored shown are Alpha (lineages B.1.1.7 + Q.*), Beta (lineage B.1.351), and Mu
(lineages B.1.621 + B.1.621.1).
• The gray bar graph (top) shows the percentage of PCR-positive samples from each 2-week time interval
that were sequenced.
• SARS-CoV-2 genome sequencing may not be a random sample of all cases. This graph does not estimate
prevalence in the population.
• Sequencing can be performed on stored patient specimens at any time, so these numbers may change as
additional specimens are sequenced.
8Estimate of proportion of variants circulating in the State of Hawaii
100
3%
24%
75
Percent of viruses sequenced
Variant
Alpha
Beta
99% 97%
50 98% 99% 99% 100% 100% 100% 99% 99% Delta
97%
Mu
Omicron
76% Other
25
3%
0
14 −2
8
−1
1
−2
5
−0
9 23 06 20 04 18 01 15
8− 8 09 9 0 0− 1− 1− 2− 2− 1− 1−
−0 −0 1− −0 −1 −1 −1 −1 −1 −1 −0 −0
21 21 2 21 21 21 21 21 21 21 22 22
20 20 20 20 20 20 20 20 20 20 20 20
2−week period ending on date
Figure Notes:
• The graph shows biweekly percentage estimates of SARS-CoV-2 variants circulating in the State of
Hawaii, grouped in two-week intervals (based on the date of sample collection).
• Not all positive SARS-CoV-2 specimens are sequenced and sequenced specimens are not a random
selection of all COVID-19 cases in the State of Hawaii. This graph has been generated only counting
samples that were selected randomly for the purpose of surveillance, to avoid over-representing the
samples that were selected for investigations of clusters.
• The last 2-week interval numbers will most likely change, as a number of samples that are currently
being processed will be added.
• Sequencing of certain specimens can be delayed for technical reasons. Therefore, the dataset used
for this report is dynamic and specimens that are newly sequenced will be added to the dataset as
sequencing occurs. Because of this, trends based on historical data can change over time.
9Variants of concern in the State of Hawaii
Variant Lineage Area of emergence Cumulative Earliest specimen Most recent specimen
cases detected collection date collection date
Delta 4736
AY.103 United States 1015 21 May 2021 23 Dec 2021
AY.44 United States 917 07 Jun 2021 27 Dec 2021
AY.3 United States 487 28 Jun 2021 02 Jan 2022
AY.25 United States 420 21 Jun 2021 04 Jan 2022
AY.54 United States 338 28 May 2021 21 Nov 2021
Other Various 199 01 Aug 2021 Sep 2021
AY.*
B.1.617.2 India 187 04 Jun 2021 16 Dec 2021
AY.100 South 169 17 Jul 2021 12 Dec 2021
Africa/Botswana
AY.25.1 South 154 08 Jul 2021 17 Dec 2021
Africa/Botswana
AY.119 United States 133 06 Jul 2021 18 Dec 2021
AY.26 United 117 07 Jun 2021 28 Dec 2021
States/Mexico
AY.117 United States 97 15 Jul 2021 17 Dec 2021
AY.47 United States 94 21 Jul 2021 07 Dec 2021
AY.122 South 74 09 Jul 2021 26 Nov 2021
Africa/Botswana
AY.39 United States 56 05 Aug 2021 15 Dec 2021
AY.118 United States 55 08 Jul 2021 17 Dec 2021
AY.13 United States 38 09 Jun 2021 16 Sep 2021
AY.20 United 37 10 Jul 2021 12 Dec 2021
States/Mexico
AY.46.4 United States 35 21 Jun 2021 06 Dec 2021
AY.14 United States 33 24 Jun 2021 17 Nov 2021
AY.2 United States 31 01 Jun 2021 19 Aug 2021
AY.75 United 30 09 Jul 2021 04 Nov 2021
States/Europe
AY.29 Japan 20 23 Jul 2021 26 Sep 2021
Omicron 1138
BA.1.1 South 822 27 Nov 2021 21 Jan 2022
Africa/Botswana
BA.1 South 307 30 Nov 2021 19 Jan 2022
Africa/Botswana
BA.2 South 8 06 Jan 2022 19 Jan 2022
Africa/Botswana
B.1.1.529 South 1 Dec 2021 Dec 2021
Africa/Botswana
Table Notes:
• Lineage “Other AY.*” represents an aggregate of different AY.* sub-lineages, each with less than 20
sequenced genomes, from the State of Hawaii.
10Variants being monitored in the State of Hawaii
Variant Lineage Area of emergence Cumulative Earliest specimen Most recent specimen
cases detected collection date collection date
Alpha 754
B.1.1.7 United Kingdom 703 21 Jan 2021 14 Aug 2021
Q.3 United States 49 21 Mar 2021 02 Sep 2021
Q.4 South 2 Apr 2021 Apr 2021
Africa/Botswana
Beta B.1.351 South Africa 19 16 Feb 2021 22 Sep 2021
Gamma 185
P.1.10 United States 81 24 Apr 2021 14 Jul 2021
P.1 Brazil 52 24 Mar 2021 21 Jul 2021
P.1.12 Peru 20 21 Mar 2021 28 Apr 2021
P.1.17 United 18 29 Mar 2021 21 Jul 2021
States/Mexico
P.1.13 United States 14 03 May 2021 07 Jun 2021
Epsilon 774
B.1.429 California 715 31 Dec 2020 03 Jun 2021
B.1.427 California 59 07 Dec 2020 05 Jun 2021
Iota B.1.526 New York 128 06 Feb 2021 23 Jul 2021
Mu 53
B.1.621 Columbia 43 03 Jun 2021 17 Sep 2021
B.1.621.1 United States 10 27 May 2021 11 Aug 2021
11Honolulu County
Total variants identified in Honolulu County
22%
22%
20
18% 18%
% of PCR−positive cases sequenced
17%
15
10
Lineage
8.2% B.1.637 AY.25.1 AY.100
7%
BA.1 AY.26 AY.103
5 BA.1.1 AY.29 AY.114
3.5% 3.7% B.1.1.7 AY.35 AY.116.1
3.2%
Q.3 AY.36 AY.117
1.2% B.1.617.2 AY.39 AY.118
0 0.33%
AY.2 AY.39.1 AY.119
AY.3 AY.43 AY.119.2
AY.3.1 AY.44 AY.120
300 AY.4 AY.46.4 AY.120.1
AY.9.2 AY.47 AY.121
AY.13 AY.48 AY.122
AY.14 AY.54 AY.125
AY.20 AY.64 AY.127
Viruses sequenced
AY.23 AY.75 B.1.351
200
AY.25 AY.81 B.1.621.1
100
0
−14 −2
8
−1
1
−2
5
−0
9
−2
3
−0
6
−2
0
−0
4
−1
8
−0
1
−1
5
08 08 09 09 10 10 11 11 12 12 01 01
21− 21− 21− 2 1− 2 1− 2 1− 2 1− 2 1− 2 1− 2 1− 22− 2 2−
20 20 20 20 20 20 20 20 20 20 20 20
2−week period ending on date
Figure Notes:
• The graph shows the total number of variants detected in Honolulu County in each 2-week interval
ending on the date shown (date represents when the specimen was collected from a patient).
• Variants of concern shown are Delta (lineages B.1.617.2 + AY.*) and Omicron (lineages B.1.1.529 +
BA.*).
• Variants being monitored shown are Alpha (lineages B.1.1.7 + Q.*), Beta (lineage B.1.351), and Mu
(lineages B.1.621 + B.1.621.1).
• The gray bar graph (top) shows the percentage of PCR-positive samples from each 2-week time interval
that were sequenced.
• SARS-CoV-2 genome sequencing may not be a random sample of all cases. This graph does not estimate
prevalence in the population.
• Sequencing can be performed on stored patient specimens at any time, so these numbers may change as
additional specimens are sequenced.
12Estimate of proportion of variants circulating in Honolulu County
100
18%
75
Percent of viruses sequenced
Variant
Alpha
93% Beta
50 100% 99% 99% 100% 100% 100% 100% 99% 99% Delta
97%
Mu
82% Omicron
Other
25
7%
0
14 −2
8
−1
1
−2
5
−0
9 23 06 20 04 18 01 15
8− 8 09 9 0 0− 1− 1− 2− 2− 1− 1−
−0 −0 1− −0 −1 −1 −1 −1 −1 −1 −0 −0
21 21 2 21 21 21 21 21 21 21 22 22
20 20 20 20 20 20 20 20 20 20 20 20
2−week period ending on date
Figure Notes:
• The graph shows biweekly percentage estimates of SARS-CoV-2 variants circulating in Honolulu County,
grouped in two-week intervals (based on the date of sample collection).
• Not all positive SARS-CoV-2 specimens are sequenced and sequenced specimens are not a random
selection of all COVID-19 cases in Honolulu County. This graph has been generated only counting
samples that were selected randomly for the purpose of surveillance of community variants, to avoid
over-representing the samples that were selected for investigations of clusters.
• Sequencing of certain specimens can be delayed for technical reasons. Therefore, the dataset used
for this report is dynamic and specimens that are newly sequenced will be added to the dataset as
sequencing occurs. Because of this, trends based on historical data can change over time.
13Variants of concern in Honolulu County
Variant Lineage Area of emergence Cumulative Earliest specimen Most recent specimen
cases detected collection date collection date
Delta 2181
AY.103 United States 582 20 Jun 2021 18 Dec 2021
AY.44 United States 361 07 Jun 2021 13 Dec 2021
AY.54 United States 235 28 May 2021 21 Nov 2021
AY.3 United States 202 28 Jun 2021 17 Dec 2021
AY.25 United States 162 21 Jun 2021 04 Jan 2022
B.1.617.2 India 94 04 Jun 2021 30 Nov 2021
AY.100 South 81 23 Jul 2021 12 Dec 2021
Africa/Botswana
Other Various 79 01 Aug 2021 Sep 2021
AY.*
AY.26 United 60 07 Jun 2021 21 Nov 2021
States/Mexico
AY.25.1 South 57 18 Jul 2021 11 Dec 2021
Africa/Botswana
AY.117 United States 50 15 Jul 2021 11 Nov 2021
AY.119 United States 48 06 Jul 2021 13 Dec 2021
AY.122 South 28 09 Jul 2021 26 Nov 2021
Africa/Botswana
AY.75 United 22 09 Jul 2021 02 Oct 2021
States/Europe
AY.39 United States 21 05 Aug 2021 09 Dec 2021
AY.14 United States 17 29 Jun 2021 17 Nov 2021
AY.118 United States 16 12 Jul 2021 30 Nov 2021
AY.29 Japan 16 23 Jul 2021 16 Sep 2021
AY.20 United 14 15 Jul 2021 07 Dec 2021
States/Mexico
AY.116.1 United States 13 02 Jul 2021 23 Oct 2021
AY.47 United States 13 21 Jul 2021 01 Dec 2021
AY.52 South 10 18 May 2021 03 Jul 2021
Africa/Botswana
Omicron 642
BA.1.1 South 506 27 Nov 2021 11 Jan 2022
Africa/Botswana
BA.1 South 136 30 Nov 2021 11 Jan 2022
Africa/Botswana
Table Notes:
• Lineage “Other AY.*” represents an aggregate of different AY.* sub-lineages, each with less than 10
sequenced genomes, from Honolulu County.
14Variants being monitored in Honolulu County
Variant Lineage Area of emergence Cumulative Earliest specimen Most recent specimen
cases detected collection date collection date
Alpha 477
B.1.1.7 United Kingdom 444 21 Jan 2021 14 Aug 2021
Q.3 United States 33 03 Apr 2021 02 Sep 2021
Beta B.1.351 South Africa 16 16 Feb 2021 22 Sep 2021
Gamma 94
P.1.10 United States 50 24 Apr 2021 13 Jul 2021
P.1 Brazil 15 24 Mar 2021 11 Jul 2021
P.1.13 United States 14 03 May 2021 07 Jun 2021
P.1.17 United 14 29 Mar 2021 20 Jul 2021
States/Mexico
P.1.12 Peru 1 Apr 2021 Apr 2021
Epsilon 346
B.1.429 California 315 05 Jan 2021 29 May 2021
B.1.427 California 31 07 Jan 2021 05 Jun 2021
Iota B.1.526 New York 26 08 Feb 2021 23 Jul 2021
Mu 21
B.1.621 Columbia 18 03 Jun 2021 28 Jul 2021
B.1.621.1 United States 3 May 2021 Aug 2021
15Maui County
Total variants identified in Maui County
21%
20
% of PCR−positive cases sequenced
15% 16%
15
14%
13% 13%
10
7.8% Lineage
BA.1 AY.39.1
5 5.3% BA.1.1 AY.44
4.6%
B.1.617.2 AY.46.4
3.5%
3% AY.2 AY.47
AY.3 AY.74
0.46% AY.4.5 AY.75
0
AY.5.3 AY.100
AY.13 AY.103
AY.20 AY.113
AY.25 AY.116.1
60 AY.25.1 AY.117
AY.26 AY.118
AY.34.2 AY.119
AY.36 AY.122
Viruses sequenced
AY.39 AY.127
40
20
0
4 8 11 5 09 23 6 0 4 8 1 5
−1 −2 − 9−
2 − 0− −0 −2 −0 −1 −0 −1
−08 −08 −09 −0 −10 −1 −11 − 11 − 12 − 12 − 01 − 01
21 21 21 21 21 21 21 21 21 21 22 22
20 20 20 20 20 20 20 20 20 20 20 20
2−week period ending on date
Figure Notes:
• The graph shows the total number of variants detected in Maui County in each 2-week interval ending
on the date shown (date represents when the specimen was collected from a patient).
• Variants of concern shown are Delta (lineages B.1.617.2 + AY.*) and Omicron (lineages B.1.1.529 +
BA.*).
• None of the variants being monitored were detected during the time periods shown.
• The gray bar graph (top) shows the percentage of PCR-positive samples from each 2-week time interval
that were sequenced.
• SARS-CoV-2 genome sequencing may not be a random sample of all cases. This graph does not estimate
prevalence in the population.
• Sequencing can be performed on stored patient specimens at any time, so these numbers may change as
additional specimens are sequenced.
16Estimate of proportion of variants circulating in Maui County
100
6%
45%
75
Percent of viruses sequenced
Variant
50 100% 100% 100% 100% 100% 100% 100% 100% 100% 100% Delta
94% Omicron
55%
25
0
14 −2
8
−1
1
−2
5
−0
9 23 06 20 04 18 01 15
8− 8 09 9 0 0− 1− 1− 2− 2− 1− 1−
−0 −0 1− −0 −1 −1 −1 −1 −1 −1 −0 −0
21 21 2 21 21 21 21 21 21 21 22 22
20 20 20 20 20 20 20 20 20 20 20 20
2−week period ending on date
Figure Notes:
• The graph shows biweekly percentage estimates of SARS-CoV-2 variants circulating in Maui County,
grouped in two-week intervals (based on the date of sample collection).
• Not all positive SARS-CoV-2 specimens are sequenced and sequenced specimens are not a random
selection of all COVID-19 cases in Maui County. This graph has been generated only counting
samples that were selected randomly for the purpose of surveillance of community variants, to avoid
over-representing the samples that were selected for investigations of clusters.
• Sequencing of certain specimens can be delayed for technical reasons. Therefore, the dataset used
for this report is dynamic and specimens that are newly sequenced will be added to the dataset as
sequencing occurs. Because of this, trends based on historical data can change over time.
17Variants of concern in Maui County
Variant Lineage Area of emergence Cumulative Earliest specimen Most recent specimen
cases detected collection date collection date
Delta 370
AY.103 United States 80 13 Jul 2021 23 Dec 2021
AY.44 United States 59 27 Jun 2021 27 Dec 2021
AY.3 United States 47 19 Jul 2021 01 Dec 2021
Other Various 34 09 Jul 2021 Oct 2021
AY.*
AY.47 United States 31 19 Aug 2021 07 Dec 2021
AY.100 South 19 22 Jul 2021 18 Nov 2021
Africa/Botswana
AY.13 United States 18 21 Jul 2021 13 Sep 2021
AY.25 United States 16 19 Aug 2021 19 Dec 2021
AY.2 United States 14 07 Jun 2021 06 Aug 2021
AY.26 United 13 03 Aug 2021 28 Oct 2021
States/Mexico
AY.25.1 South 12 24 Jul 2021 10 Dec 2021
Africa/Botswana
AY.122 South 11 19 Jul 2021 01 Oct 2021
Africa/Botswana
AY.39 United States 11 25 Sep 2021 31 Oct 2021
B.1.617.2 India 5 31 Aug 2021 16 Dec 2021
Omicron 120
BA.1.1 South 69 13 Dec 2021 11 Jan 2022
Africa/Botswana
BA.1 South 51 14 Dec 2021 09 Jan 2022
Africa/Botswana
Table Notes:
• Lineage “Other AY.*” represents an aggregate of different AY.* sub-lineages, each with less than 5
sequenced genomes, from Maui County.
18Variants being monitored in Maui County
Variant Lineage Area of emergence Cumulative Earliest specimen Most recent specimen
cases detected collection date collection date
Alpha 41
B.1.1.7 United Kingdom 39 01 Mar 2021 11 Jul 2021
Q.3 United States 2 Apr 2021 May 2021
Beta B.1.351 South Africa 1 Jul 2021 Jul 2021
Gamma 42
P.1 Brazil 22 18 Apr 2021 20 Jun 2021
P.1.12 Peru 19 21 Mar 2021 28 Apr 2021
P.1.10 United States 1 May 2021 May 2021
Epsilon 272
B.1.429 California 265 08 Jan 2021 18 May 2021
B.1.427 California 7 27 Apr 2021 10 May 2021
Iota B.1.526 New York 16 12 Mar 2021 25 Jun 2021
19Hawaii County
Total variants identified in Hawaii County
31%
30
% of PCR−positive cases sequenced
24%
20
19% 19%
18%
17%
Lineage
BA.1 AY.44
10 BA.1.1 AY.46.4
8.2% Q.3 AY.47
B.1.617.2 AY.48
5.4%
4.1% 4.5% AY.3 AY.54
3.1% AY.4.10 AY.64
0.4% AY.9.2 AY.75
0
AY.13 AY.100
AY.14 AY.103
100 AY.23 AY.110
AY.25 AY.113
AY.25.1 AY.114
AY.26 AY.117
75 AY.34.1 AY.118
AY.39 AY.119
Viruses sequenced
AY.39.1 AY.121
AY.43 AY.122
50
25
0
4 8 1 25 09 23 06 20 04 18 01 15
−1 −2 −1 9− 0− 0− 1− 1− 2− 2− 1− 1−
08 08 09 −0 −1 −1 −1 −1 −1 −1 −0 −0
2 1− 2 1− 21
−
21 21 21 21 21 21 21 22 22
20 20 20 20 20 20 20 20 2 0 2 0 2 0 2 0
2−week period ending on date
Figure Notes:
• The graph shows the total number of variants detected in Hawaii County in each 2-week interval ending
on the date shown (date represents when the specimen was collected from a patient).
• Variants of concern shown are Delta (lineages B.1.617.2 + AY.*) and Omicron (lineages B.1.1.529 +
BA.*).
• Variants being monitored shown are Alpha (lineages B.1.1.7 + Q.*).
• The gray bar graph (top) shows the percentage of PCR-positive samples from each 2-week time interval
that were sequenced.
• SARS-CoV-2 genome sequencing may not be a random sample of all cases. This graph does not estimate
prevalence in the population.
• Sequencing can be performed on stored patient specimens at any time, so these numbers may change as
additional specimens are sequenced.
20Estimate of proportion of variants circulating in Hawaii County
100
3%
75
Percent of viruses sequenced
62%
Variant
Alpha
50 99% 100% 100% 100% 100% 100% 100% 100% 100% 100%
97% Delta
Omicron
25
38%
0
14 −2
8
−1
1
−2
5
−0
9 23 06 20 04 18 01 15
8− 8 09 9 0 0− 1− 1− 2− 2− 1− 1−
−0 −0 1− −0 −1 −1 −1 −1 −1 −1 −0 −0
21 21 2 21 21 21 21 21 21 21 22 22
20 20 20 20 20 20 20 20 20 20 20 20
2−week period ending on date
Figure Notes:
• The graph shows biweekly percentage estimates of SARS-CoV-2 variants circulating in Hawaii County,
grouped in two-week intervals (based on the date of sample collection).
• Not all positive SARS-CoV-2 specimens are sequenced and sequenced specimens are not a random
selection of all COVID-19 cases in Hawaii County. This graph has been generated only counting
samples that were selected randomly for the purpose of surveillance of community variants, to avoid
over-representing the samples that were selected for investigations of clusters.
• Sequencing of certain specimens can be delayed for technical reasons. Therefore, the dataset used
for this report is dynamic and specimens that are newly sequenced will be added to the dataset as
sequencing occurs. Because of this, trends based on historical data can change over time.
21Variants of concern in Hawaii County
Variant Lineage Area of emergence Cumulative Earliest specimen Most recent specimen
cases detected collection date collection date
Delta 737
AY.44 United States 209 11 Jun 2021 16 Dec 2021
AY.3 United States 109 31 Jul 2021 16 Dec 2021
AY.103 United States 91 21 May 2021 16 Dec 2021
AY.25 United States 52 19 Jul 2021 09 Nov 2021
AY.100 South 41 17 Jul 2021 12 Nov 2021
Africa/Botswana
AY.46.4 United States 27 21 Jun 2021 06 Dec 2021
Other Various 27 12 Jul 2021 Oct 2021
AY.*
AY.118 United States 26 08 Jul 2021 27 Sep 2021
AY.25.1 South 26 11 Aug 2021 17 Dec 2021
Africa/Botswana
AY.117 United States 24 15 Aug 2021 17 Nov 2021
AY.119 United States 24 03 Aug 2021 24 Nov 2021
AY.26 United 16 24 Jun 2021 03 Dec 2021
States/Mexico
AY.122 South 15 19 Jul 2021 22 Sep 2021
Africa/Botswana
B.1.617.2 India 11 15 Jul 2021 08 Nov 2021
AY.43 Europe 9 13 Sep 2021 17 Dec 2021
AY.47 United States 8 05 Aug 2021 26 Nov 2021
AY.114 South 6 10 Oct 2021 22 Oct 2021
Africa/Botswana
AY.54 United States 6 01 Jul 2021 22 Oct 2021
AY.39 United States 5 30 Aug 2021 29 Nov 2021
AY.9.2 South 5 22 Nov 2021 09 Dec 2021
Africa/Botswana
Omicron 75
BA.1.1 South 54 10 Dec 2021 10 Jan 2022
Africa/Botswana
BA.1 South 21 10 Dec 2021 03 Jan 2022
Africa/Botswana
Table Notes:
• Lineage “Other AY.*” represents an aggregate of different AY.* sub-lineages, each with less than 5
sequenced genomes, from Hawaii County.
22Variants being monitored in Hawaii County
Variant Lineage Area of emergence Cumulative Earliest specimen Most recent specimen
cases detected collection date collection date
Alpha 66
B.1.1.7 United Kingdom 55 22 Feb 2021 16 Jul 2021
Q.3 United States 11 21 Mar 2021 20 Aug 2021
Gamma 16
P.1.10 United States 12 27 May 2021 13 Jun 2021
P.1 Brazil 3 May 2021 Jun 2021
P.1.17 United 1 Jun 2021 Jun 2021
States/Mexico
Epsilon 44
B.1.429 California 38 25 Jan 2021 26 May 2021
B.1.427 California 6 04 Feb 2021 17 May 2021
Iota B.1.526 New York 73 06 Feb 2021 07 Jul 2021
Mu B.1.621 Columbia 1 Jun 2021 Jun 2021
23Kauai County
Total variants identified in Kauai County
16%
15
14%
% of PCR−positive cases sequenced
11%
10%
10
9.1%
Lineage
BA.1
6.6% BA.1.1
B.1.617.2
5 5.3%
AY.3
3.7% 3.5% 3.6% AY.3.1
AY.4
2.1%
AY.25
AY.25.1
0.43%
0 AY.39
AY.39.1
AY.43
AY.44
30
AY.46.4
AY.47
AY.54
AY.100
Viruses sequenced
AY.103
20
AY.117
AY.119
AY.122
10
0
4 8 1 5 9 3 6 0 4 8 1 5
−1 8−
2 −1 −2 −0 −2 −0 −2 −0 −1 −0 −1
08 −0 09 09 10 10 11 11 12 12 01 01
2 1− 21 21− 21− 21− 21− 21− 21− 21− 21− 22− 22−
20 20 20 20 20 20 20 20 20 20 20 20
2−week period ending on date
Figure Notes:
• The graph shows the total number of variants detected in Kauai County in each 2-week interval ending
on the date shown (date represents when the specimen was collected from a patient).
• Variants of concern shown are Delta (lineages B.1.617.2 + AY.*) and Omicron (lineages B.1.1.529 +
BA.*).
• None of the variants being monitored were detected during the time periods shown.
• The gray bar graph (top) shows the percentage of PCR-positive samples from each 2-week time interval
that were sequenced.
• SARS-CoV-2 genome sequencing may not be a random sample of all cases. This graph does not estimate
prevalence in the population.
• Sequencing can be performed on stored patient specimens at any time, so these numbers may change as
additional specimens are sequenced.
24Estimate of proportion of variants circulating in Kauai County
100
15%
75
Percent of viruses sequenced
75%
Variant
50 100% 100% 100% 100% 100% 100% 100% 100% 100% 100% Delta
Omicron
85%
25
25%
0
14 −2
8
−1
1
−2
5
−0
9 23 06 20 04 18 01 15
8− 8 09 9 0 0− 1− 1− 2− 2− 1− 1−
−0 −0 1− −0 −1 −1 −1 −1 −1 −1 −0 −0
21 21 2 21 21 21 21 21 21 21 22 22
20 20 20 20 20 20 20 20 20 20 20 20
2−week period ending on date
Figure Notes:
• The graph shows biweekly percentage estimates of SARS-CoV-2 variants circulating in Kauai County,
grouped in two-week intervals (based on the date of sample collection).
• Not all positive SARS-CoV-2 specimens are sequenced and sequenced specimens are not a random
selection of all COVID-19 cases in Kauai County. This graph has been generated only counting
samples that were selected randomly for the purpose of surveillance of community variants, to avoid
over-representing the samples that were selected for investigations of clusters.
• Sequencing of certain specimens can be delayed for technical reasons. Therefore, the dataset used
for this report is dynamic and specimens that are newly sequenced will be added to the dataset as
sequencing occurs. Because of this, trends based on historical data can change over time.
25Variants of concern in Kauai County
Variant Lineage Area of emergence Cumulative Earliest specimen Most recent specimen
cases detected collection date collection date
Delta 232
AY.25 United States 70 16 Jul 2021 10 Nov 2021
AY.119 United States 34 28 Aug 2021 18 Dec 2021
AY.44 United States 34 01 Jul 2021 21 Dec 2021
Other Various 25 Aug 2021 Sep 2021
AY.*
AY.47 United States 19 27 Jul 2021 29 Nov 2021
AY.103 United States 16 01 Aug 2021 15 Dec 2021
B.1.617.2 India 12 09 Aug 2021 18 Oct 2021
AY.3 United States 8 30 Sep 2021 15 Dec 2021
AY.54 United States 8 06 Jul 2021 09 Nov 2021
AY.67 South 6 06 Jun 2021 29 Jun 2021
Africa/Botswana
Omicron 37
BA.1.1 South 26 15 Dec 2021 11 Jan 2022
Africa/Botswana
BA.1 South 11 16 Dec 2021 04 Jan 2022
Africa/Botswana
Table Notes:
• Lineage “Other AY.*” represents an aggregate of different AY.* sub-lineages, each with less than 5
sequenced genomes, from Kauai County.
26Variants being monitored in Kauai County
Variant Lineage Area of emergence Cumulative Earliest specimen Most recent specimen
cases detected collection date collection date
Alpha 19
B.1.1.7 United Kingdom 18 05 Apr 2021 13 Jul 2021
Q.4 South 1 Apr 2021 Apr 2021
Africa/Botswana
Gamma 2
P.1 Brazil 1 May 2021 May 2021
P.1.10 United States 1 May 2021 May 2021
Epsilon 30
B.1.429 California 28 07 Jan 2021 08 May 2021
B.1.427 California 2 Apr 2021 Apr 2021
Iota B.1.526 New York 1 Apr 2021 Apr 2021
Mu B.1.621 Columbia 1 Jul 2021 Jul 2021
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